Alonso Favela

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• Bertolet, B. L., Rodriguez, L. C., Favela, A., Allison, S. D., & Murúa, J. M. (2024). The Impact of Microbial Interactions on Ecosystem Function Intensifies Under Stress. Ecology Letters, 27(10). doi:10.1111/ele.14528
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  A major challenge in ecology is to understand how different species interact to determine ecosystem function, particularly in communities with large numbers of co-occurring species. We use a trait-based model of microbial litter decomposition to quantify how different taxa impact ecosystem function. Furthermore, we build a novel framework that highlights the interplay between taxon traits and environmental conditions, focusing on their combined influence on community interactions and ecosystem function. Our results suggest that the ecosystem impact of a taxon is driven by its resource acquisition traits and the community functional capacity, but that physiological stress amplifies the impact of both positive and negative interactions. Furthermore, net positive impacts on ecosystem function can arise even as microbes have negative pairwise interactions with other taxa. As communities shift in response to global climate change, our findings reveal the potential to predict the biogeochemical functioning of communities from taxon traits and interactions.
• Favela, A., Bohn, M., & Kent, A. (2024). Genetic variation in Zea mays influences microbial nitrification and denitrification in conventional agroecosystems. Plant and Soil. doi:10.1007/s11104-024-06720-9
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  Background and Aims: Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N2O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. Methods: To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds (Z. mays ssp. mays), ex-PVP hybrids (Z. mays ssp. mays), and teosinte (Z. mays ssp. mexicana and Z. mays ssp. parviglumis). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Results: Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N2O fluxes, with teosinte plots producing less GHG than maize plots. Conclusion: Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N2O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.
• Favela, A., Raglin, S., & Wallace, J. (2024).

  Sampling root-associated microbiome communities of maize

  . CSH Protocols, DOI: 10.1101/pdb.prot108580.
• Raglin, S., Favela, A., Laspisa, D., & Wallace, J. (2024).

   Manipulating the Maize Microbiome

  . CSH Protocols, DOI: 10.1101/pdb.prot108584.
• Capel, S. L., Allan, B. F., Favela, A., Clem, C. S., Ooi, S. K., Virrueta Herrera, S., Wilson, L. J., & Strickland, L. R. (2023). Education in the Anthropocene: assessing planetary health science standards in the USA. Proceedings of the Royal Society B: Biological Sciences, 290(2007). doi:10.1098/rspb.2023.0975
• Capel, S., Allan, B., Favela, A., Clem, C., Ooi, S., Virrueta Herrera, S., Wilson, L., & Strickland, L. (2023). Education in the Anthropocene: Assessing planetary health science standards in the USA. Proceedings of the Royal Society B: Biological Sciences, 290(2007). doi:10.1098/rspb.2023.0975
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  The environmental crises defining the Anthropocene demand ubiquitous mitigation efforts, met with collective support. Yet, disengagement and disbelief surrounding planetary health threats are pervasive, especially in the USA. This scepticism may be influenced by inadequate education addressing the scope and urgency of the planetary health crisis. We analysed current K-12 science standards related to planetary health throughout the USA, assessing their quality and potential predictors of variation. While planetary health education varies widely across the USA with respect to the presence and depth of terms, most science standards neglected to convey these concepts with a sense of urgency. Furthermore, state/territory dominant political party and primary gross domestic product (GDP) contributor were each predictive of the quality of planetary health education. We propose that a nation-wide science standard could fully address the urgency of the planetary health crisis and prevent political bias from influencing the breadth and depth of concepts covered.
• Favela, A., Bohn, M., & Kent, A. (2022). N-Cycling Microbiome Recruitment Differences between Modern and Wild Zea mays. Phytobiomes Journal, 6(2). doi:10.1094/PBIOMES-08-21-0049-R
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  Rewilding modern agricultural cultivars by reintroducing beneficial ancestral traits is a proposed approach to improve sustainability of modern agricultural systems. In this study, we compared recruitment of the rhizosphere microbiome among modern inbred maize and wild teosinte to assess whether potentially beneficial plant microbiome traits have been lost through maize domestication and modern breeding. To do this, we surveyed the bacterial and fungal communities along with nitrogen (N)-cycling functional groups in the rhizosphere of six modern domesticated maize genotypes and ancestral wild teosinte genotypes, while controlling for environmental conditions and starting soil inoculum. Using a combination of high-throughput sequencing and quantitative PCR, we found that the rhizosphere microbiomes of modern inbred and wild teosinte differed substantially in taxonomic composition, species richness, and abundance of N-cycling functional genes. Furthermore, the modern versus wild designation explained 27% of the variation in the prokaryotic microbiome, 62% of the variation in N-cycling gene richness, and 66% of N-cycling gene abundance. Surprisingly, we found that modern inbred genotypes hosted microbial communities with higher taxonomic and functional gene diversity within their microbiomes compared with ancestral genotypes. These results imply that modern maize and wild maize differ in their interaction with N-cycling microorganisms in the rhizosphere and that genetic variation exists within genus Zea to potentially “rewild” microbiome-associated traits (i.e., exudation, root phenotypes, and so on).
• York, L., Cumming, J., Trusiak, A., Bonito, G., von Haden, A., Kalluri, U., Tiemann, L., Andeer, P., Blanc-Betes, E., Diab, J., Favela, A., Germon, A., Gomez-Casanovas, N., Hyde, C., Kent, A., Ko, D., Lamb, A., Missaoui, A., Northen, T., , Pu, Y., et al. (2022). Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. Plant Phenome Journal, 5(1). doi:10.1002/ppj2.20028
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  Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.
• Favela, A., O. Bohn, M., & D. Kent, A. (2021). Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome. ISME Journal, 15(8). doi:10.1038/s41396-021-00923-z
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  Recruitment of microorganisms to the rhizosphere varies among plant genotypes, yet an understanding of whether the microbiome can be altered by selection on the host is relatively unknown. Here, we performed a common garden study to characterize recruitment of rhizosphere microbiome, functional groups, for 20 expired Plant Variety Protection Act maize lines spanning a chronosequence of development from 1949 to 1986. This time frame brackets a series of agronomic innovations, namely improvements in breeding and the application of synthetic nitrogenous fertilizers, technologies that define modern industrial agriculture. We assessed the impact of chronological agronomic improvements on recruitment of the rhizosphere microbiome in maize, with emphasis on nitrogen cycling functional groups. In addition, we quantified the microbial genes involved in nitrogen cycling and predicted functional pathways present in the microbiome of each genotype. Both genetic relatednesses of host plant and decade of germplasm development were significant factors in the recruitment of the rhizosphere microbiome. More recently developed germplasm recruited fewer microbial taxa with the genetic capability for sustainable nitrogen provisioning and larger populations of microorganisms that contribute to N losses. This study indicates that the development of high-yielding varieties and agronomic management approaches of industrial agriculture inadvertently modified interactions between maize and its microbiome.